infection.estimator: Estimate true number of COVID-19 infections based on deaths &...
In liamrevell/covid19.Explorer: A COVID-19 Explorer

infection.estimator

R Documentation

Estimate true number of COVID-19 infections based on deaths & observed cases

Description

Function to estimate the true number of COVID-19 infections through time using confirmed COVID-19 deaths, an IFR value or function specifid by the user, and observed cases.

Usage

	infection.estimator(state="Massachusetts",
		cumulative=FALSE,
		data=list(),
		delay=20,
		ifr=0.005,
		window=7,
		smooth=TRUE,
		span=c(0.12,0.3),
		percent=FALSE,
		plot=TRUE,
		bg="transparent",
		xlim=c(60,366+135),
		show.points=FALSE,
		alpha=c(0.25,0.8),
		cdr=c("sigmoid","average"),
		...)

Arguments

`state`	state or jurisdiction.
`cumulative`	show cumulative infections (logical).
`data`	list containing CDC data. If not supplied, function will create this object.
`delay`	average lag from infection to death.
`ifr`	infection-fatality-ratio/rate or function. If more than one value is specified, IFR is interpolated using LOESS smoothing.
`span`	values of `span` to be passed to `loess`. First value is for infections through time. Second value is for IFR if applicable.
`window`	window for moving average.
`smooth`	smooth estimated infections (logical).
`percent`	show values as percent of population (logical).
`plot`	create a plot (logical).
`bg`	background color for plots.
`xlim`	x-limits for the plot.
`show.points`	show points used in LOESS smoothing (logical).
`alpha`	alpha transparency levels for transparent elements of the plot.
`cdr`	model for case detection rate (CDR) through time.
`...`	optional arguments.